cnv_getLengthFraction: Calculate length fraction profile of copy number

In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description

Calculate length fraction profile of copy number

Usage

cnv_getLengthFraction(CN_data, genome_build = c("hg19", "hg38"),
  cols = c("Chromosome", "Start.bp", "End.bp", "modal_cn"),
  sample_col = "sample")

Arguments

CN_data	a QDNAseqCopyNumbers object or a list contains multiple data.frames (recommended), each data.frame stores copy-number profile for one sample with 'chromosome', 'start', 'end' and 'segVal' these four necessary columns. Of note, 'segVal' column shoule be absolute copy number values.
genome_build	genome build version, must be one of 'hg19' or 'hg38'.
cols	four characters used to specify chromosome, start position, end position and copy number value in input, respectively. Default use names from ABSOLUTE calling result.
sample_col	a character used to specify the sample column name.

Value

a data frame

Author(s)

Shixiang Wang [e-mail]

See Also

Other CNV analysis functions: cnv_autoCaptureSignatures, cnv_chooseSigNumber, cnv_derivefeatures, cnv_extractSignatures, cnv_fitMixModels, cnv_generateSbCMatrix, cnv_pipe, cnv_plotDistributionProfile, cnv_plotFeatureDistribution, cnv_plotMixComponents, cnv_plotSignatures, cnv_quantifySigExposure, cnv_readprofile

ShixiangWang/VSHunter documentation built on June 27, 2019, 4:56 p.m.